Calcium in PDB 5l8b: Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E62A

The structure of Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E62A, PDB code: 5l8b was solved by D.He, S.Hughes, S.Vanden-Hehir, A.Georgiev, K.Altenbach, E.Tarrant, C.L.Mackay, K.J.Waldron, D.J.Clarke, J.Marles-Wright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.87 / 2.21
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	98.090, 120.228, 140.358, 90.00, 95.51, 90.00
R / Rfree (%)	16.5 / 21.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E62A (pdb code 5l8b). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 24 binding sites of Calcium where determined in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E62A, PDB code: 5l8b:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 24 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E62A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E62A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:58.9 occ:1.00 OE1 A:GLU31 2.3 56.4 1.0 OE1 J:GLU31 2.4 62.9 1.0 O J:HOH216 2.5 42.8 1.0 OE1 J:GLU34 2.6 55.0 1.0 OE2 A:GLU34 2.8 55.4 1.0 CD A:GLU31 3.5 57.0 1.0 CD J:GLU31 3.5 55.1 1.0 CD J:GLU34 3.8 55.7 1.0 OE2 J:GLU31 3.9 60.2 1.0 OE2 A:GLU31 4.0 60.3 1.0 CD A:GLU34 4.0 60.6 1.0 O J:HOH220 4.1 43.4 1.0 HB3 A:GLU31 4.3 41.6 1.0 HB3 J:GLU31 4.4 38.7 1.0 HB3 A:GLU34 4.6 44.0 1.0 HA A:GLU31 4.6 46.9 1.0 OE2 J:GLU34 4.6 61.8 1.0 HB3 J:GLU34 4.6 38.8 1.0 HG2 A:GLU34 4.6 53.8 1.0 HZ3 J:TRP38 4.6 72.8 1.0 CG A:GLU31 4.7 41.5 1.0 HG2 J:GLU34 4.7 59.4 1.0 HA J:GLU31 4.7 32.6 1.0 CG J:GLU31 4.8 44.8 1.0 HH2 J:TRP38 4.8 77.3 1.0 CG J:GLU34 4.8 49.5 1.0 CG A:GLU34 4.9 44.9 1.0 HZ3 A:TRP38 4.9 82.6 1.0 CB A:GLU31 4.9 34.7 1.0 OE1 A:GLU34 4.9 60.2 1.0 CZ3 J:TRP38 4.9 60.6 1.0 HG3 A:GLU31 5.0 49.8 1.0

Calcium binding site 2 out of 24 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E62A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E62A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:67.4 occ:1.00 OE1 C:GLU31 2.4 69.0 1.0 OE1 B:GLU31 2.4 68.9 1.0 OE2 B:GLU34 2.5 55.0 1.0 O B:HOH312 2.8 39.9 1.0 OE1 C:GLU34 2.9 62.1 1.0 O C:HOH310 2.9 44.4 1.0 CD C:GLU31 3.4 57.9 1.0 CD B:GLU31 3.5 64.0 1.0 OE2 C:GLU31 3.7 59.0 1.0 CD B:GLU34 3.8 63.0 1.0 OE2 B:GLU31 3.9 70.8 1.0 CD C:GLU34 4.1 67.4 1.0 HB3 B:GLU31 4.4 45.4 1.0 HB3 C:GLU31 4.5 37.2 1.0 OE1 B:GLU34 4.5 59.0 1.0 HB3 B:GLU34 4.6 38.9 1.0 HA B:GLU31 4.6 42.6 1.0 HZ3 B:TRP38 4.6 81.3 1.0 HG2 B:GLU34 4.7 60.1 1.0 HA C:GLU31 4.7 38.7 1.0 HB3 C:GLU34 4.8 53.7 1.0 CG B:GLU31 4.8 51.5 1.0 CG C:GLU31 4.8 44.4 1.0 CG B:GLU34 4.8 50.1 1.0 HZ3 C:TRP38 4.8 91.4 1.0 HG2 C:GLU34 4.9 72.0 1.0 HH2 B:TRP38 4.9 81.6 1.0 CZ3 B:TRP38 4.9 67.8 1.0 OE2 C:GLU34 5.0 70.7 1.0 CB B:GLU31 5.0 37.8 1.0

Calcium binding site 3 out of 24 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E62A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E62A within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:57.8 occ:1.00 OE2 C:GLU91 2.5 41.1 1.0 O C:HOH313 2.5 39.6 1.0 OE1 C:GLU91 2.8 43.0 1.0 CD C:GLU91 3.0 43.9 1.0 O C:PHE89 4.3 39.4 1.0 CG C:GLU91 4.4 43.7 1.0 HA C:THR90 4.5 50.4 1.0 HG2 C:GLU91 4.6 52.4 1.0 HG3 C:GLU91 4.9 52.4 1.0 HB2 C:GLU91 5.0 46.7 1.0

Calcium binding site 4 out of 24 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E62A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E62A within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:60.4 occ:1.00 OE1 D:GLU31 2.4 62.7 1.0 OE1 E:GLU31 2.4 71.8 1.0 O D:HOH309 2.6 40.6 1.0 O E:HOH215 2.6 45.8 1.0 OE1 D:GLU34 2.8 49.0 1.0 OE2 E:GLU34 2.9 52.4 1.0 CD D:GLU31 3.5 54.8 1.0 CD E:GLU31 3.6 65.5 1.0 OE2 D:GLU31 3.9 54.1 1.0 CD D:GLU34 4.0 59.7 1.0 CD E:GLU34 4.1 51.5 1.0 OE2 E:GLU31 4.2 63.7 1.0 HB3 E:GLU31 4.3 37.5 1.0 HB3 D:GLU31 4.3 33.3 1.0 HB3 D:GLU34 4.6 45.4 1.0 HA D:GLU31 4.6 36.9 1.0 HA E:GLU31 4.7 38.5 1.0 HG2 D:GLU34 4.7 60.8 1.0 CG D:GLU31 4.8 43.6 1.0 HB3 E:GLU34 4.8 38.2 1.0 CG E:GLU31 4.8 43.9 1.0 HZ3 D:TRP38 4.8 90.8 1.0 OE2 D:GLU34 4.9 55.1 1.0 OE1 E:GLU34 4.9 48.2 1.0 CB D:GLU31 4.9 27.8 1.0 CG D:GLU34 4.9 50.7 1.0 CB E:GLU31 4.9 31.3 1.0 HG2 E:GLU34 4.9 52.9 1.0 HZ3 E:TRP38 5.0 72.7 1.0 O D:GLU31 5.0 31.5 1.0

Calcium binding site 5 out of 24 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E62A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E62A within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca201 b:61.8 occ:1.00 OE1 F:GLU31 2.3 64.8 1.0 OE1 H:GLU31 2.3 70.6 1.0 O H:HOH312 2.5 39.5 1.0 O F:HOH314 2.5 56.2 1.0 OE1 H:GLU34 2.7 58.2 1.0 O F:HOH305 2.8 44.2 1.0 OE1 F:GLU34 3.1 61.4 1.0 CD F:GLU31 3.5 53.4 1.0 CD H:GLU31 3.5 63.2 1.0 CD H:GLU34 3.9 56.5 1.0 OE2 F:GLU31 4.1 59.2 1.0 OE2 H:GLU31 4.1 64.1 1.0 HB3 F:GLU31 4.1 41.4 1.0 HB3 H:GLU31 4.2 33.5 1.0 CD F:GLU34 4.4 57.6 1.0 HB3 H:GLU34 4.5 32.4 1.0 HA H:GLU31 4.5 34.8 1.0 HG2 H:GLU34 4.6 51.7 1.0 HA F:GLU31 4.6 36.6 1.0 CG F:GLU31 4.6 38.8 1.0 CG H:GLU31 4.7 47.3 1.0 HB3 F:GLU34 4.7 44.6 1.0 HZ3 H:TRP38 4.7 77.5 1.0 OE2 H:GLU34 4.8 61.6 1.0 CB F:GLU31 4.8 34.5 1.0 CG H:GLU34 4.8 43.0 1.0 CB H:GLU31 4.8 27.9 1.0 HG3 F:GLU31 4.9 46.5 1.0 HG3 H:GLU31 4.9 56.8 1.0 HG2 F:GLU34 4.9 43.7 1.0 O H:GLU31 5.0 26.8 1.0 CZ3 H:TRP38 5.0 64.5 1.0 HZ3 F:TRP38 5.0 98.9 1.0

Calcium binding site 6 out of 24 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E62A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E62A within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca201 b:61.4 occ:1.00 OE1 G:GLU31 2.5 68.1 1.0 OE1 I:GLU31 2.5 52.6 1.0 OE2 I:GLU34 2.7 57.1 1.0 O I:HOH315 2.7 43.4 1.0 O G:HOH312 3.1 42.1 1.0 OE1 G:GLU34 3.2 60.9 1.0 CD G:GLU31 3.6 58.3 1.0 CD I:GLU31 3.6 48.1 1.0 CD I:GLU34 4.0 60.2 1.0 OE2 G:GLU31 4.0 58.8 1.0 OE2 I:GLU31 4.1 66.7 1.0 HB3 I:GLU31 4.3 35.5 1.0 CD G:GLU34 4.4 58.9 1.0 HB3 G:GLU31 4.5 26.6 1.0 HB3 I:GLU34 4.5 39.0 1.0 HZ3 I:TRP38 4.6 82.3 1.0 HA I:GLU31 4.6 37.0 1.0 HG2 I:GLU34 4.7 57.5 1.0 HA G:GLU31 4.8 37.2 1.0 O I:HOH333 4.8 45.9 1.0 OE1 I:GLU34 4.8 64.0 1.0 HB3 G:GLU34 4.8 39.4 1.0 CG G:GLU31 4.9 39.3 1.0 CG I:GLU31 4.9 38.6 1.0 CG I:GLU34 4.9 47.9 1.0 O I:GLU31 5.0 28.4 1.0 CZ3 I:TRP38 5.0 68.6 1.0 CB I:GLU31 5.0 29.6 1.0

Calcium binding site 7 out of 24 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E62A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E62A within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca202 b:71.9 occ:1.00 OE2 G:GLU61 2.6 47.2 1.0 OE1 G:GLU61 2.7 50.1 1.0 OE1 I:GLU64 2.9 44.5 1.0 CD G:GLU61 3.0 51.4 1.0 HG2 I:GLU61 3.3 51.9 1.0 HE1 G:HIS57 3.3 50.8 1.0 O I:HOH317 3.5 54.8 1.0 CD I:GLU64 3.6 41.7 1.0 CD I:GLU61 3.7 50.5 1.0 HE2 I:HIS65 3.7 38.1 1.0 OE2 I:GLU61 3.8 62.0 1.0 HE2 G:HIS57 3.9 52.4 1.0 CG I:GLU61 4.0 43.2 1.0 OE1 I:GLU61 4.1 56.3 1.0 CE1 G:HIS57 4.1 42.3 1.0 OE2 I:GLU64 4.2 52.0 1.0 HB3 I:GLU64 4.3 37.9 1.0 NE2 G:HIS57 4.4 43.7 1.0 HB3 I:GLU61 4.4 40.0 1.0 HD2 I:HIS65 4.4 35.6 1.0 NE2 I:HIS65 4.5 31.8 1.0 CG G:GLU61 4.5 45.3 1.0 HG2 I:GLU64 4.5 40.4 1.0 CG I:GLU64 4.6 33.6 1.0 HA I:GLU61 4.7 31.5 1.0 HG3 I:GLU61 4.7 51.9 1.0 CB I:GLU61 4.7 33.3 1.0 HG2 G:GLU61 4.8 54.4 1.0 CD2 I:HIS65 4.8 29.7 1.0 CB I:GLU64 4.8 31.6 1.0 HG3 G:GLU61 4.9 54.4 1.0

Calcium binding site 8 out of 24 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E62A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E62A within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca201 b:54.6 occ:0.67 O H:ASP44 2.2 30.3 1.0 O G:HOH319 2.3 45.4 1.0 O H:HOH318 2.4 39.5 1.0 C H:ASP44 3.4 32.1 1.0 HA H:ASP44 3.8 32.6 1.0 OE1 O:GLU17 3.9 70.4 1.0 HA H:ALA45 4.1 34.5 1.0 CA H:ASP44 4.2 27.1 1.0 O H:SER46 4.4 31.2 1.0 N H:ALA45 4.4 31.8 1.0 HZ1 G:LYS16 4.5 64.3 1.0 O H:VAL43 4.6 32.1 1.0 CA H:ALA45 4.6 28.7 1.0 HB3 H:ASP44 4.6 33.8 1.0 HZ2 G:LYS16 4.7 64.3 1.0 C H:ALA45 4.8 32.9 1.0 O G:VAL14 4.8 39.2 1.0 HB G:VAL14 5.0 55.7 1.0

Calcium binding site 9 out of 24 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E62A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E62A within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca202 b:70.7 occ:1.00 OE1 H:GLU61 2.7 48.1 1.0 OE2 H:GLU61 2.7 51.7 1.0 OE1 F:GLU64 2.7 49.5 1.0 CD H:GLU61 3.0 41.4 1.0 HE1 H:HIS57 3.1 52.1 1.0 CD F:GLU64 3.3 44.8 1.0 HE2 F:HIS65 3.6 42.1 1.0 HG2 F:GLU61 3.6 56.2 1.0 OE2 F:GLU64 3.6 45.7 1.0 CE1 H:HIS57 3.9 43.4 1.0 HD2 F:HIS65 4.0 40.1 1.0 HG2 F:GLU64 4.0 47.9 1.0 HE2 H:HIS57 4.1 52.3 1.0 HB3 F:GLU64 4.1 37.2 1.0 CD F:GLU61 4.2 58.6 1.0 CG F:GLU64 4.2 39.9 1.0 NE2 F:HIS65 4.3 35.0 1.0 CG F:GLU61 4.3 46.8 1.0 OE2 F:GLU61 4.4 69.5 1.0 OE1 F:GLU61 4.4 59.0 1.0 NE2 H:HIS57 4.4 43.6 1.0 HB3 F:GLU61 4.5 47.7 1.0 CD2 F:HIS65 4.5 33.5 1.0 CG H:GLU61 4.5 38.4 1.0 CB F:GLU64 4.7 31.0 1.0 HA F:GLU61 4.8 44.7 1.0 CB F:GLU61 4.9 39.7 1.0 HG2 H:GLU61 4.9 46.1 1.0 HG3 H:GLU61 4.9 46.1 1.0

Calcium binding site 10 out of 24 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E62A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E62A within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca201 b:73.6 occ:1.00 OE2 I:GLU18 2.3 75.3 1.0 CD I:GLU18 3.2 78.9 1.0 OE1 I:GLU18 3.4 95.5 1.0 HH12 I:ARG22 3.9 53.5 1.0 CG I:GLU18 4.6 49.5 1.0 NH1 I:ARG22 4.6 44.5 1.0 O I:HOH330 4.6 33.1 1.0 HG3 I:GLU18 4.7 59.4 1.0 HZ2 I:LYS16 4.8 91.5 1.0 HH11 I:ARG22 4.8 53.5 1.0 HZ1 I:LYS16 5.0 91.5 1.0

D.He, S.Hughes, S.Vanden-Hehir, A.Georgiev, K.Altenbach, E.J.Tarrant, C.L.Mackay, K.J.Waldron, D.J.Clarke, J.Marles-Wright. Structural Characterization of Encapsulated Ferritin Provides Insight Into Iron Storage in Bacterial Nanocompartments. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27529188
DOI: 10.7554/ELIFE.18972